Changes

                           --format      1                                (or 2,3)

                           --format      1                                (or 2,3)

This command will create three files :  <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2, or 3. Each of these values correspond to the three different PLINK dosage file formats (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details.

This command will create three files :  <code>OutPrefix.plink.dosage.gz</code>, <code>OutPrefix.fam</code>, and <code>OutPrefix.map</code>. The <code>.fam</code> and <code>.map</code> formats are described [http://zzz.bwh.harvard.edu/plink/data.shtml#map here]. The <code>--format</code> parameter can take values 1, 2, or 3. Each of these values correspond to the three different PLINK dosage file formats (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which will need to be manually edited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[#Converting Chromosome X Files | Converting Chromosome X Files]] for details.

== Convert to MaCH Files ==

== Convert to MaCH Files ==